Data and code from: Universal bacterial clade dynamics dominate under predation despite altered phenotypes and mutation targets

Recent studies have revealed bacterial genome-wide evolution to be complex
and dynamic even in a constant environment, characterized by the emergence
of new clades competing or temporarily coexisting as each clade undergoes
evolutionary change. Previous studies on predator-prey dynamics tracking
simple ecological and phenotypic metrics have shown predation to
fundamentally alter prey evolution, facilitating defense evolution
followed by coevolution and frequency-dependent selection between defended
and undefended prey genotypes. Here, we sought to consolidate these fields
by examining genome-wide evolution in five bacterial prey species
separately subjected to long-term evolution under ciliate predation. We
hypothesized that the presence of predation could change the pattern of
clonal dynamics, for example, by more frequently producing selective
sweeps if predation-defense-related mutations are under strong selection.
For all species, we found mutational signals of prey adaptation, with
phenotypic data and genomic mutation targets demonstrating changes in
composition between the experimental treatments. Intriguingly, despite
higher variant counts, overall temporal clade dynamics across the
coevolved prey species were strikingly similar to those of bacteria
evolving alone, with constant emergence, competition and quasi-stable
coexistence of clades. This study shows that long-term molecular evolution
in bacterial prey under predation is more interesting and less predictable
than we might expect based on existing coevolutionary theories.